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SkinEdit is a simple graphics editor optimized for making Minecraft skins. It got many features to make it easier for beginners to understand how Minecraft skinning works as well as all the features even experienced skinners need. With over HALF A MILLION downloads so far the latest alpha fixes many bugs and adds a new imrpoved tool feature.
For more information read the forum topic (linked at the bottom, click read more)

IF YOU GET STUCK LAUNCHING OR HAVE PROBLEMS WITH THE PREVIEWER TRY TO DOWNLOAD THIS FIX: Solidfiles.com

Instalation:

Make sure you have Java installed (if you can play Minecraft you have Java installed already)

Download the file, preferably with the download button, but if you have problems use the mirror

Open the compressed file (.zip). Your computer should be able to do this without external programs, but 7-zip and WinRAR can handle it as well.

Put the files anywhere on your computer, but note that it will be a lot easier to get 3D preview working if you put it in a folder you have write access in (For example, under Windows 'My Document' or 'Desktop' works. You can put it in a sub-folder. Under Linux any folder under your home folder should work. Just make sure to get all files if you want to get the most out of SkinEdit (such as the 'backgrounds' folder for additional backgrounds)

Just doubleclick 'MCSkinEdit.jar' (Might be displayed as 'MCSkinEdit'). SkinEdit should now launch

To get 3D preview working, just click ok when SkinEdit prompts you to enter the URL for the previewer. This is only done the first time you launch SkinEdit.

SkinEdit is mostly tested under Windows 7, but should work in Windows XP, Windows Vista, Windows 7, newer versions of OSX and all graphical Linux versions (Tested on Ubuntu).

Downloading the 3D previewer manually:
This is normally not needed!
Sometimes the 3D previewer won't get downloaded automatically. This is usually the result of not being able to write to the current location. If you are experienced with your operating system you can launch SkinEdit as administrator which probably will allow it to download the previewer. This is only needed once. But, launching java programs with administrator status in Windows requires command prompt usage and therefore I will explain how to do it the easy way:

Right click on the following link and click "Save As" or "Save Link As" depending on what browser you use. This might not work in Internet Explorer due to a flaw in it. In that case you have to use another browser. Minecraft.net

When you saved the file move it to the same place as MCSkinEdit.jar. Next time you launch SkinEdit it will find the file and you'll get 3D preview.

Key features:

Easy to understand for a new skinner

Realtime 3D preview supported (please note that this uses code made by notch)

It has the features you need the most. Burn and dodge for shading, flood fill and large brushes to paint large areas

Fully functional undo and redo system

Add details easilly with PartPicker

Planned features:

Load a skin from a website

Direct uploading to some imagehost as well as directly applying the skin (using Notch safe method for this)

Screenshots:
Loaded the default skin

Playing around with the new shading functions

Tested the mac support on a friends macbook

Backgrounds:
Since alpha 3 pre 4 you can add your own backgrounds and use. Some of the best backgrounds will be listed here for download!
For a background to work the width must be divideable by 64 and the height by 32.

Mobs reskin pack (by: Notch, Patrik Swedman)
Unfortunately you can't preview them property, but at least you can use SkinEdit for some of your re-skin needs. Includes both a gray scale and a color version of every mob image (except zombie) in the size 640x320.
Bug: The color ones isn't scaled. A fix will be released later on.DownloadMirror

EiETemplate (by: The Eie)
A alternative to the normal backgrounds. Best viewed with a bright background and with around 70% alpha. (Will be included in alpha 3 pre 5)DownloadMirror

PartPicker:
PartPicker was introduced in alpha 3 pre 5 and is a way to easily add details to already existing skins, but if you're crazy enough you could create a entire skin with this feature. PartPicker simply lets you glue parts of a skin onto your own skin, such as glasses, a pair of jeans and why not your clan logo?
To add a new part you simply put it in the 'parts' folder. The file format must be .png and the size must be 64x32px. The area that isn't a part of the skin must be completely transparent (alpha 0).

Feedback and support:
You can get feedback and support in the forum topic

It is java based. The screenshot is from Ubuntu but I mostly develop on Windows 7. Should run on mac as well but I have a hard time finding macs to test on (but alpha 3 pre 7 which is this version has been tested and should fully work on all macs that run java 5)

Still can't get this working. SkinEdit Alpha 3 pre 7, Mac OSX 10.6.8
Just updated java, downloaded both the settings.xml and skintest2.jar which were said to fix the 'stuck on loading' problem, and nothing has changed. Please help!